Magnesium in PDB 6d9s: The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)

All present enzymatic activity of The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase):
2.4.2.8;

The structure of The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase), PDB code: 6d9s was solved by K.A.Satyshur, K.Dubiel, B.Anderson, C.Wolak, J.L.Keck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.20 / 2.11
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.611, 82.611, 174.916, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.4

The binding sites of Magnesium atom in the The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) (pdb code 6d9s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase), PDB code: 6d9s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:71.6 occ:1.00 O1C A:G4P201 2.0 64.5 1.0 O A:HOH325 2.0 84.5 1.0 OD1 A:ASP159 2.1 72.0 1.0 O A:HOH336 2.1 79.4 1.0 O1D A:G4P201 2.2 76.6 1.0 O A:HOH343 2.3 55.5 1.0 CG A:ASP159 3.1 55.9 1.0 PC A:G4P201 3.4 72.5 1.0 HH22 A:ARG165 3.4 64.2 1.0 OD2 A:ASP159 3.5 58.6 1.0 H1' A:G4P201 3.5 0.8 1.0 PD A:G4P201 3.6 0.7 1.0 HH12 A:ARG165 3.6 80.6 1.0 O A:HOH346 3.7 79.1 1.0 H A:ASP159 3.8 66.7 1.0 O3C A:G4P201 3.8 84.5 1.0 HN21 A:G4P201 3.9 97.0 1.0 NH2 A:ARG165 4.1 53.2 1.0 O A:HOH351 4.2 88.2 1.0 NH1 A:ARG165 4.2 66.9 1.0 O A:ASP159 4.3 66.1 1.0 O3' A:G4P201 4.3 84.6 1.0 O A:HOH304 4.3 76.7 1.0 N3 A:G4P201 4.4 61.0 1.0 O2D A:G4P201 4.4 64.4 1.0 C1' A:G4P201 4.4 84.6 1.0 CB A:ASP159 4.4 63.3 1.0 O2C A:G4P201 4.5 76.3 1.0 H4' A:G4P201 4.5 0.7 1.0 O4' A:G4P201 4.5 61.9 1.0 O A:HOH355 4.6 60.3 1.0 N A:ASP159 4.6 55.3 1.0 CZ A:ARG165 4.6 61.6 1.0 O3D A:G4P201 4.6 67.6 1.0 HB3 A:ASP159 4.7 76.2 1.0 HH21 A:ARG165 4.7 64.2 1.0 N2 A:G4P201 4.8 80.5 1.0 HH11 A:ARG165 4.9 80.6 1.0 C A:ASP159 4.9 66.7 1.0 CA A:ASP159 4.9 63.4 1.0 C4' A:G4P201 4.9 0.5 1.0

Magnesium binding site 2 out of 2 in the The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The (P)Ppgpp-Bound Crystal Structure of Hprt (Hypoxanthine Phosphoribosyltransferase) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:0.5 occ:1.00 O B:HOH333 2.0 0.8 1.0 OD1 B:ASP159 2.0 0.0 1.0 O2D B:G4P201 2.1 0.8 1.0 OD2 B:ASP159 2.1 0.8 1.0 O B:HOH301 2.2 89.4 1.0 NH2 B:ARG165 2.2 0.3 1.0 CG B:ASP159 2.2 0.9 1.0 HH21 B:ARG165 2.5 0.3 1.0 O B:HOH306 3.0 67.6 1.0 CZ B:ARG165 3.1 87.0 1.0 O1C B:G4P201 3.1 0.1 1.0 HH12 B:ARG165 3.1 77.3 1.0 NH1 B:ARG165 3.5 64.2 1.0 PD B:G4P201 3.5 58.5 1.0 CB B:ASP159 3.6 80.5 1.0 HB3 B:ASP159 3.7 96.9 1.0 O B:HOH339 3.8 73.4 1.0 H B:ASP159 3.9 65.7 1.0 O3D B:G4P201 4.0 61.8 1.0 O3C B:G4P201 4.2 67.2 1.0 HB2 B:ASP159 4.2 96.9 1.0 NE B:ARG165 4.2 64.2 1.0 HH11 B:ARG165 4.2 77.3 1.0 PC B:G4P201 4.3 93.9 1.0 OE2 B:GLU162 4.3 74.3 1.0 HE B:ARG165 4.3 77.3 1.0 H B:GLU162 4.4 79.3 1.0 HA B:GLU162 4.5 79.5 1.0 N B:ASP159 4.5 54.5 1.0 CA B:ASP159 4.6 65.4 1.0 O B:HOH349 4.6 72.3 1.0 O1D B:G4P201 4.7 67.6 1.0 OE1 B:GLU162 4.7 69.5 1.0 CD B:GLU162 4.7 63.0 1.0 O B:ASP159 4.8 62.3 1.0 HN21 B:G4P201 4.9 0.8 1.0 C B:ASP159 4.9 59.7 1.0 HD2 B:LYS43 5.0 79.0 1.0

B.W.Anderson, K.Liu, C.Wolak, K.Dubiel, F.She, K.A.Satyshur, J.L.Keck, J.D.Wang. Evolution of (P)Ppgpp-Hprt Regulation Through Diversification of An Allosteric Oligomeric Interaction. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31552824
DOI: 10.7554/ELIFE.47534